ap_cutoff_selection: Cutoff selection

In cekehe/rappp: QC, data transformation and visualization for PAPP

Cutoff selection

Description

Select cutoff based on the slope of the density of scores per antigen.

Usage

ap_cutoff_selection(x, cutoffs, slope_cutoff = -0.5, offset = 0.1, bw = 0.1)

Arguments

x	List of scoring values with two levels per element: level one = assay data sets ; level two = bead subsets (e.g. wih and w/o controls). It is recommended to use to element Scoring in the output from ap_scoring).
cutoffs	data.frame with at least two columns: - One column named score with the desired cutoffs to use - One column named xmad with the corresponding MAD cutoff values It is recommended is to use the Cutoff_key element in the output from ap_scoring).
slope_cutoff	Arbitrary slope cutoff value. Can be chosen freely.
offset	Offset used to prevent script from finding the peak (as slope = 0 there).
bw	Bandwidth for density funciton, default set to 0.1.

Details

A cutoff will be selected for each antigen based on the distribution of the scores for the antigen. The algorithm will search for a local min nearest the highest peak in a density plot using bandwidth=0.1.

The input values should be scoring values, and structured as a list (preferably the output from function ap_scoring()), even if only one data set is used (see examples in ap_mads).

Value

List with two main elements

[[1]] Density output used for cutoff selection, with same structure as input list.

[[2]] Calculated antigen specific cutoffs, with same structure as input list.

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.